Anomalous roughness with system size dependent local roughness exponent

We note that in a system far from equilibrium the interface roughening may depend on the system size which plays the role of control parameter. To detect the size effect on the interface roughness, we study the scaling properties of rough interfaces formed in paper combustion experiments. Using paper sheets of different width \lambda L, we found that the turbulent flame fronts display anomalous multi-scaling characterized by non universal global roughness exponent \alpha and the system size dependent spectrum of local roughness exponents,\xi_q, whereas the burning fronts possess conventional multi-affine scaling. The structure factor of turbulent flame fronts also exhibit unconventional scaling dependence on \lambda These results are expected to apply to a broad range of far from equilibrium systems, when the kinetic energy fluctuations exceed a certain critical value.Comment: 33 pages, 16 figure

Combining machine learning with structurebased protein design to predict and engineer post-Translational modifications of proteins

Post-Translational modifications (PTMs) of proteins play a vital role in their function and stability. These modifications influence protein folding, signaling, protein-protein interactions, enzyme activity, binding affinity, aggregation, degradation, and much more. To date, over 400 types of PTMs have been described, representing chemical diversity well beyond the genetically encoded amino acids. Such modifications pose a challenge to the successful design of proteins, but also represent a major opportunity to diversify the protein engineering toolbox. To this end, we first trained artificial neural networks (ANNs) to predict eighteen of the most abundant PTMs, including protein glycosylation, phosphorylation, methylation, and deamidation. In a second step, these models were implemented inside the computational protein modeling suite Rosetta, which allows flexible combination with existing protocols to model the modified sites and understand their impact on protein stability as well as function. Lastly, we developed a new design protocol that either maximizes or minimizes the predicted probability of a particular site being modified. We find that this combination of ANN prediction and structure-based design can enable the modification of existing, as well as the introduction of novel, PTMs. The potential applications of our work include, but are not limited to, glycan masking of epitopes, strengthening protein-protein interactions through phosphorylation, as well as protecting proteins from deamidation liabilities. These applications are especially important for the design of new protein therapeutics where PTMs can drastically change the therapeutic properties of a protein. Our work adds novel tools to Rosetta s protein engineering toolbox that allow for the rational design of PTMs

Load assessment and analysis of impacts in multibody systems

The evaluation of contact forces during an impact requires the use of continuous force-based methods. An accurate prediction of the impact force demands the identification of the contact parameters on a case-by-case basis. In this paper, the preimpact effective kinetic energy (Formula presented.) is put forward as an indicator of the intensity of the impact force along the contact normal direction. This represents a part of the total kinetic energy of the system that is associated with the subspace of constrained motion defined by the impact constraints at the moment of contact onset. Its value depends only on the mechanical parameters and the configuration of the system. We illustrate in this paper that this indicator can be used to characterize the impact force intensity. The suitability of this indicator is confirmed by numerical simulations and experimentsPostprint (author's final draft

ExWave: A high performance discontinuous Galerkin solver for the acoustic wave equation

A high performance implementation of a discontinuous Galerkin discretization with explicit Runge–Kutta and arbitrary derivative (ADER) time integration schemes is presented to solve the acoustic wave equation. For ADER, both a global and a local time stepping variant is supplied. The implementation is based on the matrix-free framework of the deal.II finite element library providing efficient evaluation routines for quadrilaterals and hexahedra. The implementation is generic and its applicability is demonstrated for academic examples as well as real world problems like urban acoustics. We present the physical and numerical problem description, the general code structure, and the design principles. MSC: 65M60, 65Y20, 68N19, Keywords: Matrix-free methods, Discontinuous Galerkin methods, Acoustic wave equatio